Population Genome-wide Analysis of Geographically Distant Isolates of the Bee Pathogen Nosema Ceranae

Abstract

Microsporidia are a peculiar phylum of ancestral fungal relatives who have remained enigmatic and largely unknown up until the end of last century. Recent research has revealed some clues about their parasitic life style, and provided some answers regarding their basic biology. Research done as part of my Master’s degree has combined next generation genome sequencing and with powerful bioinformatics analyses to make new contributions in the field of microsporidian biology. In this dissertation, I will focus on describing the results of my main project, a population genomic study of an economically important microsporidium, Nosema ceranae. Infections from this species have been associated with recent global declines in the populations of western honeybees (Apis mellifera). Despite the outstanding economic and ecological threat that N. ceranae may represent for honeybees worldwide, many aspects of its biology, including its mode of reproduction, propagation and ploidy, are either very unclear or unknown. In my thesis, I aimed to expand our knowledge of N. ceranae biology by sequencing the genome of 8 isolates (i.e. a population of spores isolated from one single beehive) of this species harvested from 8 geographically distant beehives, and by investigating their level of polymorphism. Consistent with previous analysis performed using single gene sequences, my analyses exposed a very high genetic diversity within each isolate, but also very little hive-specific polymorphism. My investigations on the nature, location and distribution of this variation revealed that that beehives around the globe are infected by a population of N. ceranae cells that are polyploid (4n or more) and clonal. Furthermore, phylogenetic analyses I performed using genome-wide SNP data extracted from these parasites and mitochondrial sequences from their hosts all failed to support the current geographical structure of our isolates, suggesting that the isolates we analyzed have probably spread through human intervention. Altogether, research done as part of my Master’s degree has resulted in essential breakthroughs in our biological understanding of an economically and ecologically important parasite of honeybees.